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- PDB-4qhu: Crystal Structure of IL-17A/Fab6785 complex -

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Basic information

Entry
Database: PDB / ID: 4qhu
TitleCrystal Structure of IL-17A/Fab6785 complex
Components
  • Fab6785 heavy chain
  • Fab6785 light chain
  • Interleukin-17A
KeywordsIMMUNE SYSTEM / antibody-antigen interaction / receptor differentiation / Molecular asymmetry / cystine knot / cytokine IL-17 / IL-17RA / IL-17RC
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / negative regulation of inflammatory response to wounding / intestinal epithelial structure maintenance / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / negative regulation of inflammatory response to wounding / intestinal epithelial structure maintenance / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / fibroblast activation / positive regulation of bicellular tight junction assembly / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / response to wounding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell-cell signaling / gene expression / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / external side of plasma membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLuo, J. / Gilliland, G.L. / Malia, T. / Obmolova, G. / Teplyakov, A.
CitationJournal: To be Published
Title: IL-17A Asymmetry in a Complex with a Neutralizing Antibody Fab6785 Reveals a Potential Mechanism of Receptor Differentiation
Authors: Luo, J. / Gilliland, G.L. / Malia, T. / Obmolova, G. / Teplyakov, A.
History
DepositionMay 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab6785 light chain
H: Fab6785 heavy chain
A: Fab6785 light chain
B: Fab6785 heavy chain
C: Interleukin-17A
D: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,65217
Polymers123,6766
Non-polymers97611
Water20,6991149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17780 Å2
ΔGint-179 kcal/mol
Surface area46800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.210, 64.000, 145.600
Angle α, β, γ (deg.)90.00, 95.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules CD

#3: Protein Interleukin-17A / IL-17 / IL-17A / Cytotoxic T-lymphocyte-associated antigen 8 / CTLA-8


Mass: 15202.122 Da / Num. of mol.: 2 / Mutation: K70Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16552

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Antibody , 2 types, 4 molecules LAHB

#1: Antibody Fab6785 light chain


Mass: 22767.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: homo sapiens (human)
#2: Antibody Fab6785 heavy chain


Mass: 23868.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: homo sapiens (human)

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Non-polymers , 4 types, 1160 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium acetate, 12% PEG 5000, 0.2 M lithium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 28, 2009
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 67999 / Num. obs: 67999 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.2
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4612 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 6.1 / % possible all: 91.7

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.299 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 3449 5.07 %RANDOM
Rwork0.1711 ---
obs0.1734 67988 99.32 %-
all-67999 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8014 0 56 1149 9219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038286
X-RAY DIFFRACTIONf_angle_d0.73111288
X-RAY DIFFRACTIONf_dihedral_angle_d12.0722965
X-RAY DIFFRACTIONf_chiral_restr0.0281275
X-RAY DIFFRACTIONf_plane_restr0.0031454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2001-2.23030.2426980.21072163216385
2.2303-2.26210.26281370.19326072607100
2.2621-2.29590.25461490.194325812581100
2.2959-2.33180.26131330.195725342534100
2.3318-2.370.24411510.193526292629100
2.37-2.41080.24541530.189525202520100
2.4108-2.45470.25061310.187326222622100
2.4547-2.50190.22831280.189625472547100
2.5019-2.5530.24331440.193926082608100
2.553-2.60850.25391360.195725722572100
2.6085-2.66910.25041470.197225712571100
2.6691-2.73590.28781410.196325782578100
2.7359-2.80980.22551680.184325762576100
2.8098-2.89250.23511510.181325942594100
2.8925-2.98590.22251470.183525422542100
2.9859-3.09260.25841200.177826182618100
3.0926-3.21640.23071340.176326272627100
3.2164-3.36270.20071230.164926302630100
3.3627-3.540.1931370.157625922592100
3.54-3.76170.19511400.160326142614100
3.7617-4.0520.18781200.145226252625100
4.052-4.45950.17381350.134726092609100
4.4595-5.10420.17471440.133526272627100
5.1042-6.42830.17521340.163826602660100
6.4283-48.31030.20261480.18262693269399

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